Swarmv2:Highly-scalable and high-resolution amplicon clustering

Mahé, Frédéric, Rognes, Torbjørn, Quince, Christopher, de Vargas, Colomban and Dunthorn, Micah (2015) Swarmv2:Highly-scalable and high-resolution amplicon clustering. PeerJ, 2015 (12). ISSN 2167-8359

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Abstract

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarmv1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs.Here we present Swarmv2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individualOTUs as two-dimensional networks.

Item Type: Article
Additional Information: Publisher Copyright: © 2015 Mahé et al.
Uncontrolled Keywords: barcoding,environmental diversity,molecular operational taxonomic units,neuroscience(all),biochemistry, genetics and molecular biology(all),agricultural and biological sciences(all) ,/dk/atira/pure/subjectarea/asjc/2800
Faculty \ School: Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 09 Sep 2022 09:31
Last Modified: 22 Sep 2022 19:31
URI: https://ueaeprints.uea.ac.uk/id/eprint/88019
DOI: 10.7717/peerj.1420

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